bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1534/g3.117.042655

Manipulating the Mitochondrial Genome To Enhance Cattle Embryo Development
Cited by: 15
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 9 years ago

Core Binding Factors are essential for ovulation, luteinization, and female fertility in mice
Cited by: 10
Author(s): Somang Lee-Thacker, Hayce Jeon, Yohan Choi, Ichiro Taniuchi, Takeshi Takarada, Yukio Yoneda, Che Myong Ko, Misung Jo
Software Mentions: 1
Published: over 6 years ago

10.1534/g3.116.038075

A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in Mimulus
Cited by: 23
Author(s): Kimmy A Stanton, Patrick P. Edger, Joshua R. Puzey, Taliesin J Kinser, Philip A Cheng, Daniel M. Vernon, Nancy R. Forsthoefel, Arielle M. Cooley
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2018.01565

Comparative Transcriptomics of Cold Growth and Adaptive Features of a Eury- and Steno-Psychrophile
Cited by: 31
Author(s): Isabelle Raymond-Bouchard, Julien Tremblay, Ianina Altshuler, Charles W. Greer, Lyle G. Whyte
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2018.02418

Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11
Cited by: 7
Author(s): Annereinou Dijkstra, Marjo Starrenburg, Tilman Todt, Sacha A. F. T. van Hijum, Jeroen Hugenholtz, Peter A. Bron
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.24260

ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer
Cited by: 21
Author(s): Amanda B. Pilling, Jihye Kim, Adriana Estrada-Bernal, Qiong Zhou, Anh‐Tuan Le, Katherine R. Singleton, Lynn E. Heasley, Aik Choon Tan, James DeGregori, Robert C. Doebele
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmicb.2018.00877

Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle
Cited by: 16
Author(s): Marcos H. de Moraes, Emanuel Becerra Soto, Isaí Salas González, Prerak Desai, Chu Wu, Steffen Porwollik, Michael McClelland, Max Teplitski
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.563139

tpo3 and dur3, Aspergillus fumigatus Plasma Membrane Regulators of Polyamines, Regulate Polyamine Homeostasis and Susceptibility to Itraconazole
Cited by: 6
Author(s): Mingcong Chen, Guowei Zhong, Sha Wang, Jun Zhu, Lei Tang, Lei Li
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2020.00460

Investigating the Role of FlhF Identifies Novel Interactions With Genes Involved in Flagellar Synthesis in Campylobacter jejuni
Cited by: 11
Author(s): Xiaofei Li, Fangzhe Ren, Guoqiang Cai, Pingyu Huang, Qinwen Chai, Ozan Gundogdu, Xinan Jiao, Jinlin Huang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67476-7

Co-expression based cancer staging and application
Cited by: 7
Author(s): Xiangchun Yu, Sha Cao, Yi Zhou, Zhezhou Yu, Ying Xu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67635-w

Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Cited by: 7
Author(s): Jaya Gupta, Sagar Thapa, Madhulika Verma, Ritu Som, Kakali Mukherjee
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.01264

Yeast Assimilable Nitrogen Concentrations Influence Yeast Gene Expression and Hydrogen Sulfide Production During Cider Fermentation
Cited by: 10
Author(s): Yangbo Song, Patrick A. Gibney, Lailiang Cheng, Shuwen Liu, Gregory M. Peck
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66387-x

Combined PLT and NE to predict the prognosis of patients with locally advanced cervical cancer
Cited by: 5
Author(s): Han Wang, Wen-Ming Chen, Yong-Heng Zhou, Jianping Shi, Yongzhen Huang, Wenjie Wang
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2019.01873

Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph
Cited by: 12
Author(s): Carlo R. Carere, Ben McDonald, Hanna Peach, Chris Greening, Daniel J. Gapes, Christophe Collet, Matthew B. Stott
Software Mentions: 1
Published: about 7 years ago

10.1186/s12918-016-0374-0

Small RNA profiles in soybean primary root tips under water deficit
Cited by: 31
Author(s): Yun Zheng, Vandana K. Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais‐Brière, Andrew Farmer, Gregory D. May, Martín Crespi, Henry T. Nguyen, Ramanjulu Sunkar
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-020-68339-x

Transcriptional and in silico analyses of MIF cytokine and TLR signalling interplay in the LPS inflammatory response of Ciona robusta
Cited by: 9
Author(s): Vincenzo Arizza, Angela Bonura, Laura La Paglia, Alfonso Urso, Annalisa Pinsino, Aiti Vizzini
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2014.00430

Wolbachia is not all about sex: male-feminizing Wolbachia alters the leafhopper Zyginidia pullula transcriptome in a mainly sex-independent manner
Cited by: 12
Author(s): Hosseinali Asgharian, Peter L. Chang, Peter John Mazzoglio, Ilaria Negri
Software Mentions: 1
Published: about 12 years ago

10.1155/2021/9917060

Increased EHHADH Expression Predicting Poor Survival of Osteosarcoma by Integrating Weighted Gene Coexpression Network Analysis and Experimental Validation
Cited by: 1
Author(s): Juncheng Cui, Guoliang Yi, Jinxin Li, Yangtao Li, Dongyang Qian
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.01765

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose
Cited by: 18
Author(s): Sabrina Giaretta, Laura Treu, Veronica Vendramin, Vinícius da Silva Duarte, Armin Tarrah, Stefano Campanaro, Viviana Corich
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2018.00859

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8
Cited by: 62
Author(s): Helen L. Hayden, Keith W. Savin, Jenny Wadeson, Vadakattu V. S. R. Gupta, Pauline M. Mele
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.01643

Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils
Cited by: 54
Author(s): Liu Jin, Barbara J. Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W. Liu, Julien Tremblay, Kerry LaForge, Michael P. Schellenberg, Chantal Hamel, Luke D. Bainard
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.00150

Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Cited by: 35
Author(s): Murugesan Sivaranjani, Katarzyna Leskinen, Chairmandurai Aravindraja, Päivi Saavalainen, Shunmugiah Karutha Pandian, Mikael Skurnik, Arumugam Veera Ravi
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-019-1987-z

Frequent genetic aberrations in the cell cycle related genes in mucosal melanoma indicate the potential for targeted therapy
Cited by: 18
Author(s): Lina Xu, Zhiyuan Cheng, Chuanliang Cui, Xiaowen Wu, Huan Yu, Jun Guo, Yan Kong
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-69434-9

Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens
Cited by: 18
Author(s): Xiaoxiang Yang, Lei Zhang, Yunjia Xiang, Lei Du, Xiaoqin Huang, Yong Liu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67760-6

A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma
Cited by: 21
Author(s): Mei Liu, Qiufeng Pan, Ruihai Xiao, Yi Yu, Wenbao Lu, Longwang Wang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-68637-4

Cellular, mitochondrial and molecular alterations associate with early left ventricular diastolic dysfunction in a porcine model of diabetic metabolic derangement
Cited by: 14
Author(s): Ilkka Heinonen, Oana Sorop, Bas M. van Dalen, Rob C I Wüst, Jens van de Wouw, Vincent J. de Beer, Yanti Octavia, Richard van Duin, Youri Hoogstrate, Lau Blonden, Milla Alkio, Katja Anttila, Andrew Stubbs, Jolanda van der Velden, Daphne Merkus, Dirk J. Duncker
Software Mentions: 1
Published: about 6 years ago

10.1155/2018/7538204

An Efficient Feature Selection Strategy Based on Multiple Support Vector Machine Technology with Gene Expression Data
Cited by: 25
Author(s): Ying Zhang, Qingchun Deng, Wenbin Liang, Xuan Zou
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-70484-2

Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma
Cited by: 50
Author(s): Shengjie Bai, Yinying Wu, Yanli Yan, Shuai Shao, Jiangzhou Zhang, Jiaxin Liu, Baojun Hui, Rui Li, Hailin Ma, Xiaozhi Zhang, Juan Ren
Software Mentions: 1
Published: about 6 years ago

10.1155/2021/5585884

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress
Cited by: 5
Author(s): Jine Fu, Lingyun Wan, Lina Song, Lili He, Ni Jiang, Hairong Long, Juan Huo, Xiaowen Ji, Ying Wei, Shugen Wei, Limei Pan
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/8579651

Identification of Long Noncoding RNA Biomarkers for Hepatocellular Carcinoma Using Single-Sample Networks
Cited by: 2
Author(s): Xiaoqing Yu, Jingsong Zhang, Rui Yang, Chun Li
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-70932-z

Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach
Cited by: 6
Author(s): Mihir Mandal, Haktan Suren, Chandrasekar S. Kousik
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-71050-6

RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva
Cited by: 3
Author(s): Qing Liu, Nan Chen, Huabo Chen, Yusen Huang
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: over 10 years ago

10.1155/2019/5023125

Aluminum Responsive Genes in Flax (Linum usitatissimum L.)
Cited by: 10
Author(s): George S. Krasnov, Alexey A. Dmitriev, Alexander V. Zyablitsin, Tatiana A. Rozhmina, А. А. Жученко, Parfait Kezimana, Anastasiya V. Snezhkina, Maria S. Fedorova, Roman O. Novakovskiy, Elena N. Pushkova, Liubov V. Povkhova, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2021.651744

Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Cited by: 11
Author(s): Carlo R. Carere, Kiel Hards, Kathryn Wigley, Luke Carman, Karen M. Houghton, Gregory M. Cook, Matthew B. Stott
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-72117-0

A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Cited by: 9
Author(s): James A. Budnick, Lauren M. Sheehan, Miranda. J. Ginder, Kevin C. Failor, Julia. M. Perkowski, John. F. Pinto, Kirsten A. Kohl, Lin Kang, Pawel Michalak, Li Luo, Jason E. Heindl, Clayton C. Caswell
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2019.02452

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities
Cited by: 10
Author(s): Qin Ma, Heike Bücking, Jose L. Gonzalez-Hernandez, Senthil Subramanian
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.01266

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere
Cited by: 54
Author(s): Ubiana C. Silva, Julliane Dutra Medeiros, Laura Hora Rios Leite, Daniel Morais, Sara Cuadros-Orellana, Carlos A. S. Oliveira, U. G. de P. Lana, E. A. Gomes, Vera Lúcia dos Santos
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-72448-y

Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion
Cited by: 6
Author(s): Katsuya Sakai, Takumi Nishiuchi, Shoichiro Tange, Yoshinori Suzuki, Seiji Yano, Minoru Terashima, Takeshi Suzuki, Kunio Matsumoto
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2016.00880

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms
Cited by: 41
Author(s): Rachel E. Diner, Sarah M. Schwenck, John P. McCrow, Hong Zheng, Andrew E. Allen
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2018.00299

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse
Cited by: 22
Author(s): Diego Javier Jiménez, Maryam Chaib De Mares, Joana Falcão Salles
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-74049-1

De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Cited by: 8
Author(s): Nisha Dhiman, Anil Kumar, Dinesh Kumar, Amita Bhattacharya
Software Mentions: 1
Published: about 6 years ago

10.1155/2021/6692544

miR-145-5p Inhibits the Proliferation, Migration, and Invasion of Esophageal Carcinoma Cells by Targeting ABRACL
Cited by: 11
Author(s): Shengming Fan, Pei Chen, Shugang Li
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.00848

Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth
Cited by: 11
Author(s): Alvaro Fuertes, Sergio Pérez-Burillo, Iñigo Apaolaza, Yvonne Vallès, M. Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-74789-0

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale
Cited by: 23
Author(s): Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2016.01279

Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51
Cited by: 55
Author(s): Wesley J. Mair, Wei‐Wei Deng, Jonathan Mullins, Samuel West, Penghao Wang, Naghmeh Besharat, Simon R. Ellwood, Richard P. Oliver, Francisco J. López-Ruiz
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.02569

Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems
Cited by: 39
Author(s): Mina Bižić-Ionescu, Danny Ionescu, Hans‐Peter Grossart
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.26071

Intratumor heterogeneity ofHMCN1mutant alleles associated with poor prognosis in patients with breast cancer
Cited by: 16
Author(s): Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-73164-3

Assessing the prognostic value of stemness-related genes in breast cancer patients
Cited by: 5
Author(s): Wenjie Wang, Han Wang, Meng-Sen Wang, Yongzhen Huang, Yuan Ma, Jie Qi, Jianping Shi, Wei Li
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-75537-0

Enhanced FGFR3 activity in postmitotic principal neurons during brain development results in cortical dysplasia and axonal tract abnormality
Cited by: 5
Author(s): Jui-Yen Huang, Bruna Baumgarten Krebs, Marisha Lynn Miskus, May Lin Russell, Eamonn Patrick Duffy, Jason Michael Graf, Hui-Chen Lu
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2015.00631

Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation
Cited by: 36
Author(s): Zhenfeng Liu, Amy E. Koid, Ramón Terrado, Victoria Campbell, David A. Caron, Karla B. Heidelberg
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2018.00189

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium
Cited by: 10
Author(s): Nathan G. Walworth, Michael D. Lee, Christopher Suffridge, Pingping Qu, Fei-Xue Fu, Mak A. Saito, Eric A. Webb, Sergio A. Sañudo‐Wilhelmy, David A. Hutchins
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.539702

Calcineurin Regulates Conidiation, Chlamydospore Formation and Virulence in Fusarium oxysporum f. sp. lycopersici
Cited by: 10
Author(s): Yi-Hsuan Hou, Li-Hang Hsu, Hsuan-Fu Wang, Yu-Hsin Lai, Ying-Lien Chen
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2019.01622

Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease
Cited by: 13
Author(s): Ammar Aziz, Derek S. Sarovich, Elizabeth Nosworthy, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan, Erin P. Price, Tegan M. Harris
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-76171-6

Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
Cited by: 6
Author(s): Sera Jung, Jong Hee Lee
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-021-02922-w

Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis
Cited by: 16
Author(s): Jingqi Suo, Chenlu Zhou, Zhikai Zeng, Xipu Li, Hongwu Bian, Junhui Wang, Maoyan Zhu, Ning Han
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.00752

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae
Cited by: 30
Author(s): Mohammad Moniruzzaman, Eric R. Gann, Steven W. Wilhelm
Software Mentions: 1
Published: over 8 years ago

10.1039/c9bm01481k

Heparin-based hydrogel scaffolding alters the transcriptomic profile and increases the chemoresistance of MDA-MB-231 triple-negative breast cancer cells
Cited by: 12
Author(s): Nidhi Menon, Ha X. Dang, Udaya Sree Datla, Maryam Moarefian, Christopher B. Lawrence, Christopher A. Maher, Coleen Jones
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2016.01465

Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole
Cited by: 7
Author(s): Michele Cristine Ribeiro de Freitas, Juliana Alves Resende, Alessandra Barbosa Ferreira-Machado, Guadalupe del Rosario Quispe Saji, Ana Tereza Ribeiro de Vasconcelos, Vânia Lúcia da Silva, Marisa Fabiana Nicolás, Cláudio Galuppo Diniz
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.02308

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells
Cited by: 7
Author(s): Gaofeng Ni, Sebastian Canizales, Elias Broman, Domenico Simone, Viraja R. Palwai, Daniel Lundin, Margarita López-Fernández, Tom Sleutels, Mark Dopson
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2020.01096

ClpV3 of the H3-Type VI Secretion System (H3-T6SS) Affects Multiple Virulence Factors in Pseudomonas aeruginosa
Cited by: 14
Author(s): Yanqi Li, Lin Chen, Pansong Zhang, Anjali Y. Bhagirath, Kangmin Duan
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-74594-9

Involvement of neutrophils in machineries underlying the rupture of intracranial aneurysms in rats
Cited by: 19
Author(s): Mika Kushamae, Haruka Miyata, Makoto Shirai, Kampei Shimizu, Mieko Oka, Hirokazu Koseki, Yu Abekura, Isao Ono, Kazuhiko Nozaki, Tohru Mizutani, Tomohiro Aoki
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2019.02640

Diversity Distribution and Assembly Mechanisms of Planktonic and Benthic Microeukaryote Communities in Intertidal Zones of Southeast Fujian, China
Cited by: 20
Author(s): Jie Kong, Ying Wang, Alan Warren, Bangqin Huang, Ping Sun
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2018.03266

Multi-Method Characterization of the Human Circulating Microbiome
Cited by: 103
Author(s): Emma Whittle, Martin O. Leonard, Rebecca D Harrison, Timothy W. Gant, Daniel Tonge
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13104-021-05648-y

The brain transcriptome of the wolf spider, Schizocosa ocreata
Cited by: 0
Author(s): Daniel Stribling, Peter L. Chang, Justin E. Dalton, Christopher A. Conow, Malcolm F. Rosenthal, Eileen A. Hebets, Rita M. Graze, Michelle N. Arbeitman
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2015.01262

Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Cited by: 42
Author(s): Hui Wang, Jürgen Tomasch, Victoria Michael, Sabin Bhuju, Michael Jarek, Jörn Petersen, Irene Wagner‐Döbler
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-020-77177-w

Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L.
Cited by: 6
Author(s): Lu Guo, Zhihua Wu, Peng Yan, Xiuhua Shang, Yi Xie, R. J. Arnold
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-77598-7

Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding
Cited by: 7
Author(s): Selisha A. Sooklal, Phelelani T. Mpangase, Mihai-Silviu Tomescu, Shaun Aron, Scott Hazelhurst, Robert H. Archer, Karl Rumbold
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2020.594243

Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease
Cited by: 4
Author(s): Dawit A. Yohannes, Andrea de Kauwe, Katri Kaukinen, Kalle Kurppa, Markku Mäki, Robert P. Anderson, Sten Linnarsson, Dario Greco, Päivi Saavalainen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2019.02394

IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia
Cited by: 35
Author(s): Liang Li, Mei Xue, Fang Fu, Liang Yin, Li Feng, Pinghuang Liu
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-77293-7

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato
Cited by: 13
Author(s): Koichi Suematsu, Masaru Tanaka, Rie Kurata, Kai Yu
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.26401

Exploiting the transcriptional specificity of the alpha-methylacyl-CoA racemase AMACR promoter for the molecular imaging of prostate cancer
Cited by: 4
Author(s): Mariya Shapovalova, Julia Davydova, Christine Henzler, Mark Daniel, Scott M. Dehm, Christopher A. Warlick, Aaron M. LeBeau
Software Mentions: 1
Published: almost 8 years ago

10.3389/fimmu.2018.01372

CD19+CD24hiCD38hi B Cells Are Expanded in Juvenile Dermatomyositis and Exhibit a Pro-Inflammatory Phenotype After Activation Through Toll-Like Receptor 7 and Interferon-α
Cited by: 60
Author(s): Christopher Piper, Meredyth G Ll Wilkinson, Claire T. Deakin, G. Otto, S Dowle, Chantal L. Duurland, Stuart Adams, Emiliano Marasco, Elizabeth C. Rosser, Anna Radziszewska, Rita Carsetti, Yiannis Ioannou, Philip L. Beales, Daniel Kelberman, David Isenberg, Claudia Mauri, Kiran Nistala, Lucy R. Wedderburn
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-78976-x

Early pregnancy maternal progesterone administration alters pituitary and testis function and steroid profile in male fetuses
Cited by: 13
Author(s): Katarzyna Siemienowicz, Yili Wang, Magda Marečková, Junko Nio‐Kobayashi, Paul A. Fowler, Michael T. Rae, W. Colin Duncan
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-78781-6

Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus
Cited by: 6
Author(s): Chiaki Hori, Naoki Takata, Pui Ying Lam, Yuki Tobimatsu, Soichiro Nagano, Jenny C. Mortimer, Dan Cullen
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.26377

Targeting the Wnt/β-catenin pathway in human osteosarcoma cells
Cited by: 43
Author(s): Fang Fang, Ashley M. VanCleave, Ralph Helmuth, Haydee M. Torres, Kirby Rickel, Hannah Wollenzien, Hongli Sun, Erliang Zeng, Jing Zhao, Jianning Tao
Software Mentions: 1
Published: almost 8 years ago

10.3390/biology10040312

Differential Expression of the Tetraspanin CD9 in Normal and Leukemic Stem Cells
Cited by: 0
Author(s): Rachid Lahlil, Maurice Scrofani, Anne Aries, Philippe Hénon, Bernard Drénou
Software Mentions: 1
Published: over 5 years ago

10.1002/2211-5463.13059

Quantitative comparison of the mRNA content of human iPSC‐derived motor neurons and their extracellular vesicles
Cited by: 4
Author(s): Kentaro Otake, Keiko Adachi-Tominari, Hiroaki Nagai, Masayo Saito, Osamu Sano, Yoshihiko Hirozane, Hidehisa Iwata
Software Mentions: 1
Published: over 5 years ago

10.1096/fj.201701558R

Macrophage‐derived extracellular vesicles mediate smooth muscle hyperplasia: role of altered miRNA cargo in response to HIV infection and substance abuse
Cited by: 45
Author(s): Himanshu Sharma, Mahendran Chinnappan, Stuti Agarwal, Pranjali Dalvi, Sumedha Gunewardena, Amy O’Brien-Ladner, Navneet K. Dhillon
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-020-80837-6

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium
Cited by: 6
Author(s): Aboozar Soorni, Amir Mohammad Akrami, Reza Abolghasemi, Maryam Vahedi
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-80280-7

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae
Cited by: 15
Author(s): He Meng, Mingming Sun, Zipeng Jiang, Yutong Liu, Yu Sun, Dan Liŭ, Caihong Jiang, Min Ren, Guangdi Yuan, Wenlong Yu, Qi Sheng Feng, Aiguo Yang, Lei Cheng, Yuanying Wang
Software Mentions: 1
Published: almost 6 years ago

10.12688/f1000research.9094.2

Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury
Cited by: 6
Author(s): Liam M. Koehn, Natassya M. Noor, Qing Dong, Sing-Yan Er, Lachlan D. Rash, Glenn F. King, Katarzyna M. Dzięgielewska, NR Saunders, Mark D. Habgood
Software Mentions: 1
Published: almost 10 years ago

10.3390/biology9050109

Brain Control Reproduction by the Endocrine System of Female Blue Gourami (Trichogaster trichopterus)
Cited by: 4
Author(s): Gad Degani
Software Mentions: 1
Published: over 6 years ago

10.12688/f1000research.3928.2

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Cited by: 68
Author(s): Zhiyin Dai, Julie Sheridan, Linden J. Gearing, Darcy Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O’Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 1
Published: about 12 years ago

10.18632/oncotarget.27493

DOT1L inhibition is lethal for multiple myeloma due to perturbation of the endoplasmic reticulum stress pathway
Cited by: 10
Author(s): Caroline Dafflon, Swann Gaulis, Louise Barys, Karen Kapur, Vanessa Cornacchione, Lina Schukur, Sebastian Bergling, Elisabetta Traggiai, Selina Jansky, Leon Hellmann, Barbara Schacher Engstler, Gráinne Kerr, Antoine DeWeck, David A. Ruddy, Ulrike Naumann, Frédéric Stauffer, Christoph Gaul, Ying Lin, Éric Billy, Andreas Weiss, Francesco Hofmann, Moriko Ito, Ralph Tiedt
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-81164-0

Androgen receptor and its splice variant, AR-V7, differentially induce mRNA splicing in prostate cancer cells
Cited by: 9
Author(s): Manjul Rana, Jianrong Dong, Matthew J. Robertson, Cristian Coarfa, Nancy L. Weigel
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40164-021-00230-5

Blocking siglec-10hi tumor-associated macrophages improves anti-tumor immunity and enhances immunotherapy for hepatocellular carcinoma
Cited by: 26
Author(s): Nan Xiao, Xiao‐Dong Zhu, Kangshuai Li, Yifan Chen, Xuefeng Li, Bin Xu, Ming Lei, Jiejie Xu, Hui–Chuan Sun
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-80680-9

GATA3 somatic mutations are associated with clinicopathological features and expression profile in TCGA breast cancer patients
Cited by: 14
Author(s): Fahimeh Afzaljavan, Ayeh Sadat Sadr, Sevtap Savas, Alireza Pasdar
Software Mentions: 1
Published: almost 6 years ago

10.1186/1756-0500-5-506

The bench scientist's guide to statistical analysis of RNA-Seq data
Cited by: 35
Author(s): Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram
Software Mentions: 1
Published: about 14 years ago

10.1093/emph/eow010

Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee
Cited by: 5
Author(s): Alexander S. Advani, Annie Y. Chen, Courtney C. Babbitt
Software Mentions: 1
Published: almost 11 years ago

10.3390/biology10070607

Life-On-Hold: Lanthanoids Rapidly Induce a Reversible Ametabolic State in Mammalian Cells
Cited by: 0
Author(s): A.M. Subbot, Sabina Kondratieva, Novikov Ia, Natalia Gogoleva, О. С. Козлова, I. V. Chebotar, Guzel Gazizova, Anastasia V. Ryabova, М. А. Воронцова, Takahiro Kikawada, Elena Shagimardanova, Oleg Gusev
Software Mentions: 1
Published: over 5 years ago

10.1186/s13293-018-0173-y

Orphan receptor GPR37L1 contributes to the sexual dimorphism of central cardiovascular control
Cited by: 12
Author(s): James L. Coleman, Margaret A Mouat, Jianxin Wu, Nikola Jancovski, Jaspreet K Bassi, Andrea Y. Chan, David T. Humphreys, Nadine Mrad, Ze‐Yan Yu, Tony Ngo, Siiri E. Iismaa, Cristobal G. dos Remedios, Michael P. Feneley, Andrew M. Allen, Robert M. Graham, Nicola J. Smith
Software Mentions: 1
Published: over 8 years ago

10.1111/eva.13024

Age‐dependent expression of cancer‐related genes in a long‐lived seabird
Cited by: 4
Author(s): Richard Meitern, Jérôme Fort, Mathieu Giraudeau, Kalev Rattiste, Elin Sild, Tuul Sepp
Software Mentions: 1
Published: over 6 years ago

10.1186/s13227-016-0050-x

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Cited by: 42
Author(s): Jesús F. Peña, Alexandre Alié, Daniel J. Richter, Lingyu Wang, Noriko Funayama, Scott Nichols
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-021-81856-7

Freshwater mussels (Unionidae) brought into captivity exhibit up-regulation of genes involved in stress and energy metabolism
Cited by: 10
Author(s): Ieva Roznere, Brandon T. Sinn, Marymegan Daly, G. Thomas Watters
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-82284-3

Notch signaling-modified mesenchymal stem cells improve tissue perfusion by induction of arteriogenesis in a rat hindlimb ischemia model
Cited by: 7
Author(s): Shigeru Miyagawa, Shigeru Miyagawa, Takuji Kawamura, Takashi Shibuya, Kenichi Watanabe, Tomoya Nakagawa, Akira Harada, Dai Chida, Yoshiki Sawa
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568